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MolNFT v1 · #126795 · protein

Crystal structure of an O2-tolerant [nife]-hydrogenase from ralstonia eutropha in a its as-isolated high-pressurized form

5MDJ: “Crystal structure of an O2-tolerant [nife]-hydrogenase from ralstonia eutropha in a its as-isolated…”. X-ray diffraction, 6 ligands (NFV, SF4, F3S). MolNFT v1 #126795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5MDJ
Type
protein
Length
859 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
P31891, P31892
Ligands
NFV, SF4, F3S, F4S, MG, CL

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
L—protein598—P31891
S—protein261—P31892

Ligands and binding sites

  • NFV · Ni-Fe oxidized active center · ligand · chains L
  • SF4 · Iron/sulfur cluster · ligand · chains S
  • F3S · FE3-S4 cluster · ligand · chains L, S
  • F4S · FE4-S3 cluster · ligand · chains L, S
  • MG · Magnesium ion · metal · chains L
  • CL · Chloride ion · ion · chains S

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

  • 5MDJ · Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in a its… · the same entry in another collection · chain L against L, TM-score 1.00
  • P31891 · AlphaFold monomer V2.0 prediction for uptake hydrogenase large subunit (P31891) · a predicted model of the same protein · chain L against A, TM-score 1.00
  • P31892 · AlphaFold monomer V2.0 prediction for uptake hydrogenase small subunit (P31892) · a predicted model of the same protein · chain S against A, TM-score 0.99

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